• using R Under development (unstable) (2025-09-15 r88835)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘MiscMetabar/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘MiscMetabar’ version ‘0.14.3’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘mia’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘MiscMetabar’ can be installed ... [2m/14m] OK See the install log for details.
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [29s/127s] OK
• checking whether the package can be loaded with stated dependencies ... [28s/181s] OK
• checking whether the package can be unloaded cleanly ... [29s/215s] OK
• checking whether the namespace can be loaded with stated dependencies ... [27s/128s] OK
• checking whether the namespace can be unloaded cleanly ... [29s/106s] OK
• checking loading without being on the library search path ... [27s/86s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [141s/366s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [16s/43s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4m/11m] ERROR Running examples in ‘MiscMetabar-Ex.R’ failed The error most likely occurred in: > ### Name: upset_pq > ### Title: Make upset plot for phyloseq object. > ### Aliases: upset_pq > > ### ** Examples > > if (requireNamespace("ComplexUpset")) { + upset_pq(data_fungi_mini, + fact = "Height", width_ratio = 0.2, + taxa_fill = "Class" + ) + } Loading required namespace: ComplexUpset Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ). Number of non-matching ASV 0 Number of matching ASV 45 Number of filtered-out ASV 0 Number of kept ASV 45 Number of kept samples 137 Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. ℹ The deprecated feature was likely used in the ComplexUpset package.   Please report the issue at   <https://github.com/krassowski/complex-upset/issues>. Warning: themes$intersections_matrix is not a valid theme. Please use `theme()` to construct themes. Warning: `legend.margin` must be specified using `margin()` ℹ For the old behavior use `legend.spacing` Warning: themes$intersections_matrix is not a valid theme. Please use `theme()` to construct themes. Warning: selected_theme is not a valid theme. Please use `theme()` to construct themes. Warning: `legend.margin` must be specified using `margin()` ℹ For the old behavior use `legend.spacing` Warning: selected_theme is not a valid theme. Please use `theme()` to construct themes. Error in `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`: ! Can't merge the `axis.text` theme element. Caused by error: ! `object` must be an <S7_object>, not a S3<element_text/element> Backtrace:      ▆   1. ├─MiscMetabar::upset_pq(...)   2. │ └─ComplexUpset::upset(...)   3. │ └─S7:::Ops.S7_object(...)   4. │ ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)   5. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)   6. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])   7. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)   8. │ └─base_ops[[.Generic]](e1, e2)   9. │ ├─S7::S7_dispatch()  10. │ └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)  11. │ └─ggplot2:::add_ggplot(e1, e2, e2name)  12. │ ├─ggplot2::ggplot_add(object, p, objectname)  13. │ └─ggplot2:::ggplot_add.default(object, p, objectname)  14. │ └─ggplot2::update_ggplot(object = object, plot = plot, ...)  15. │ ├─S7::S7_dispatch()  16. │ └─ggplot2 (local) `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`(object = `<theme>`, plot = `<ggplt2::>`, ...)  17. │ ├─S7::set_props(plot, theme = add_theme(plot@theme, object))  18. │ └─ggplot2:::add_theme(plot@theme, object)  19. │ ├─rlang::try_fetch(...)  20. │ │ ├─base::tryCatch(...)  21. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)  22. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])  23. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)  24. │ │ └─base::withCallingHandlers(...)  25. │ └─ggplot2::merge_element(t2[[item]], t1[[item]])  26. │ ├─S7::S7_dispatch()  27. │ └─ggplot2 (local) `method(merge_element, list(ggplot2::element, class_any))`(...)  28. │ └─S7::props(old, idx)  29. │ └─S7::check_is_S7(object)  30. │ └─base::stop(msg, call. = FALSE)  31. └─base::.handleSimpleError(...)  32. └─rlang (local) h(simpleError(msg, call))  33. └─handlers[[1L]](cnd)  34. └─cli::cli_abort(...)  35. └─rlang::abort(...) Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [206s/321s] ERROR   Running ‘spelling.R’   Running ‘testthat.R’ [205s/318s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(MiscMetabar)   Loading required package: phyloseq   Loading required package: ggplot2   Loading required package: dada2   Loading required package: Rcpp   Loading required package: dplyr      Attaching package: 'dplyr'      The following object is masked from 'package:testthat':          matches      The following objects are masked from 'package:stats':          filter, lag      The following objects are masked from 'package:base':          intersect, setdiff, setequal, union      Loading required package: purrr      Attaching package: 'purrr'      The following object is masked from 'package:testthat':          is_null      >   > test_check("MiscMetabar")   Starting 2 test processes   [ FAIL 2 | WARN 2 | SKIP 74 | PASS 81 ]      ══ Skipped tests (74) ══════════════════════════════════════════════════════════   • On CRAN (74): 'test_adonis.R:1:1', 'test_controls.R:7:3',     'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',     'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',     'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',     'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',     'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',     'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:16:5',     'test_deseq2_edgeR.R:25:3', 'test_deseq2_edgeR.R:48:5',     'test_deseq2_edgeR.R:59:3', 'test_figures_biplot.R:14:3',     'test_figures_biplot.R:52:3', 'test_figures_misc.R:11:3',     'test_figures_misc.R:19:3', 'test_figures_misc.R:26:3',     'test_figures_misc.R:35:3', 'test_figures_beta_div.R:22:3',     'test_figures_beta_div.R:73:5', 'test_figures_beta_div.R:92:3',     'test_figures_beta_div.R:102:5', 'test_figures_beta_div.R:159:5',     'test_figures_beta_div.R:209:3', 'test_figures_beta_div.R:241:5',     'test_figures_beta_div.R:259:5', 'test_figures_beta_div.R:289:5',     'test_figures_beta_div.R:314:3', 'test_figures_beta_div.R:346:3',     'test_figures_beta_div.R:355:3', 'test_figures_beta_div.R:387:3',     'test_figures_beta_div.R:402:3', 'test_figures_beta_div.R:414:3',     'test_figures_summary_plot.R:9:3', 'test_figures_summary_plot.R:19:3',     'test_figures_summary_plot.R:28:3', 'test_krona.R:7:3',     'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',     'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',     'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',     'test_figures_taxo.R:379:3', 'test_figures_taxo.R:414:3',     'test_phyloseq_class.R:10:3', 'test_phyloseq_class.R:51:3',     'test_phyloseq_class.R:95:3', 'test_rw.R:8:3', 'test_rw.R:24:3',     'test_rw.R:39:3', 'test_subset.R:7:3', 'test_subset.R:18:3',     'test_table_functions.R:6:3', 'test_table_functions.R:19:3',     'test_table_functions.R:34:5', 'test_table_functions.R:47:5',     'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:84:3',     'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',     'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',     'test_misc.R:30:3', 'test_misc.R:97:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test_figures_beta_div.R:72:5'): graph_test_pq works ───────────────   `graph_test_pq(data_fungi_mini, fact = "Tree_name")` produced warnings.   ── Failure ('test_figures_beta_div.R:258:5'): upset_pq works with data_fungi dataset ──   `suppressMessages(upset_pq(data_fungi_mini, "Height"))` produced warnings.      [ FAIL 2 | WARN 2 | SKIP 74 | PASS 81 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [53s/135s] ERROR Error(s) in re-building vignettes: --- re-building ‘MiscMetabar.Rmd’ using rmarkdown Quitting from MiscMetabar.Rmd:66-68 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'MiscMetabar.Rmd' failed with diagnostics: Can't merge the `axis.text` theme element. Caused by error: ! `object` must be an <S7_object>, not a S3<element_text/element> --- failed re-building ‘MiscMetabar.Rmd’ SUMMARY: processing the following file failed:   ‘MiscMetabar.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [21s/64s] OK
• checking HTML version of manual ... [12s/41s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 3 ERRORs